MRG: TOPUP update

nipype/interfaces/afni/base.py

@@ -144,7 +144,7 @@ def set_default_output_type(cls, outputtype):
         else:
             raise AttributeError('Invalid AFNI outputtype: %s' % outputtype)
 
-    def _overload_extension(self, value):
+    def _overload_extension(self, value, name=None):
         path, base, _ = split_filename(value)
         return os.path.join(path, base + Info.outputtype_to_ext(self.inputs.outputtype))
 

nipype/interfaces/afni/preprocess.py

@@ -367,7 +367,7 @@ class AutoTcorrelate(AFNICommand):
     output_spec = AFNICommandOutputSpec
     _cmd = '3dAutoTcorrelate'
 
-    def _overload_extension(self, value):
+    def _overload_extension(self, value, name=None):
         path, base, ext = split_filename(value)
         if ext.lower() not in [".1d", ".nii.gz", ".nii"]:
             ext = ext + ".1D"
@@ -1924,7 +1924,7 @@ class AFNItoNIFTI(AFNICommand):
     input_spec = AFNItoNIFTIInputSpec
     output_spec = AFNICommandOutputSpec
 
-    def _overload_extension(self, value):
+    def _overload_extension(self, value, name=None):
         path, base, ext = split_filename(value)
         if ext.lower() not in [".1d", ".nii.gz", ".1D"]:
             ext = ext + ".nii"

nipype/interfaces/base.py

@@ -1492,13 +1492,13 @@ def _filename_from_source(self, name):
             _, _, ext = split_filename(retval)
             if trait_spec.keep_extension and ext:
                 return retval
-            return self._overload_extension(retval)
+            return self._overload_extension(retval, name)
         return retval
 
     def _gen_filename(self, name):
         raise NotImplementedError
 
-    def _overload_extension(self, value):
+    def _overload_extension(self, value, name=None):
         return value
 
     def _list_outputs(self):

nipype/interfaces/fsl/base.py

@@ -239,7 +239,7 @@ def _gen_fname(self, basename, cwd=None, suffix=None, change_ext=True,
                                 use_ext=False, newpath=cwd)
         return fname
 
-    def _overload_extension(self, value):
+    def _overload_extension(self, value, name=None):
         return value + Info.output_type_to_ext(self.inputs.output_type)
 
 

nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py

@@ -16,20 +16,28 @@ def test_ApplyTOPUP_inputs():
     ignore_exception=dict(nohash=True,
     usedefault=True,
     ),
-    in_files=dict(argstr='%s',
+    in_files=dict(argstr='--imain=%s',
     mandatory=True,
+    sep=',',
     ),
-    in_index=dict(argstr='%s',
+    in_index=dict(argstr='--inindex=%s',
     mandatory=True,
+    sep=',',
     ),
-    in_topup=dict(argstr='--topup=%s',
-    mandatory=True,
+    in_topup_fieldcoef=dict(argstr='--topup=%s',
+    copyfile=False,
+    requires=['in_topup_movpar'],
+    ),
+    in_topup_movpar=dict(copyfile=False,
+    requires=['in_topup_fieldcoef'],
     ),
     interp=dict(argstr='--interp=%s',
     ),
     method=dict(argstr='--method=%s',
     ),
-    out_base=dict(argstr='--out=%s',
+    out_corrected=dict(argstr='--out=%s',
+    name_source=['in_files'],
+    name_template='%s_corrected',
     ),
     output_type=dict(),
     terminal_output=dict(mandatory=True,

nipype/interfaces/fsl/tests/test_auto_TOPUP.py

@@ -8,8 +8,14 @@ def test_TOPUP_inputs():
     config=dict(argstr='--config=%s',
     usedefault=True,
     ),
-    encoding_direction=dict(),
+    encoding_direction=dict(argstr='--datain=%s',
+    mandatory=True,
+    requires=['readout_times'],
+    xor=['encoding_file'],
+    ),
     encoding_file=dict(argstr='--datain=%s',
+    mandatory=True,
+    xor=['encoding_direction'],
     ),
     environ=dict(nohash=True,
     usedefault=True,
@@ -33,15 +39,31 @@ def test_TOPUP_inputs():
     numprec=dict(argstr='--numprec=%s',
     ),
     out_base=dict(argstr='--out=%s',
+    hash_files=False,
+    name_source=['in_file'],
+    name_template='%s_base',
     ),
     out_corrected=dict(argstr='--iout=%s',
+    hash_files=False,
+    name_source=['in_file'],
+    name_template='%s_corrected',
     ),
     out_field=dict(argstr='--fout=%s',
+    hash_files=False,
+    name_source=['in_file'],
+    name_template='%s_field',
     ),
     out_logfile=dict(argstr='--logout=%s',
+    hash_files=False,
+    keep_extension=True,
+    name_source=['in_file'],
+    name_template='%s_topup.log',
     ),
     output_type=dict(),
-    readout_times=dict(),
+    readout_times=dict(mandatory=True,
+    requires=['encoding_direction'],
+    xor=['encoding_file'],
+    ),
     regrid=dict(argstr='--regrid=%d',
     ),
     scale=dict(argstr='--scale=%d',
@@ -69,7 +91,6 @@ def test_TOPUP_outputs():
     out_fieldcoef=dict(),
     out_logfile=dict(),
     out_movpar=dict(),
-    out_topup=dict(),
     )
     outputs = TOPUP.output_spec()
 

nipype/workflows/dmri/fsl/epi.py

@@ -370,7 +370,7 @@ def topup_correction( name='topup_correction' ):
     >>> nipype_epicorrect = topup_correction('nipype_topup')
     >>> nipype_epicorrect.inputs.inputnode.in_file_dir = 'epi.nii'
     >>> nipype_epicorrect.inputs.inputnode.in_file_rev = 'epi_rev.nii'
-    >>> nipype_epicorrect.inputs.inputnode.encoding_direction = 'y'
+    >>> nipype_epicorrect.inputs.inputnode.encoding_direction = ['y', 'y-']
     >>> nipype_epicorrect.inputs.inputnode.ref_num = 0
     >>> nipype_epicorrect.run() # doctest: +SKIP
 
@@ -400,7 +400,6 @@ def topup_correction( name='topup_correction' ):
     outputnode = pe.Node( niu.IdentityInterface(
                           fields=['out_fieldcoef',
                                   'out_movpar',
-                                  'out_topup',
                                   'out_enc_file',
                                   'epi_corrected'
                           ]), name='outputnode'
@@ -424,10 +423,11 @@ def topup_correction( name='topup_correction' ):
                      ,(combin,        merged, [('out', 'in_files')] )
                      ,(merged,         topup, [('merged_file','in_file')])
                      ,(inputnode,      topup, [('encoding_direction','encoding_direction'),('readout_times','readout_times') ])
-                     ,(topup,     applytopup, [('out_topup','in_topup'),('out_enc_file','encoding_file')])
+                     ,(topup,     applytopup, [('out_fieldcoef','in_topup_fieldcoef'),('out_movpar','in_topup_movpar'),
+                                               ('out_enc_file','encoding_file')])
                      ,(combin2,   applytopup, [('out','in_files')] )
                      ,(topup,     outputnode, [('out_fieldcoef','out_fieldcoef'),('out_movpar','out_movpar'),
-                                               ('out_topup','out_topup'),('out_enc_file','out_enc_file') ])
+                                               ('out_enc_file','out_enc_file') ])
                      ,(applytopup,outputnode, [('out_corrected','epi_corrected')])
                      ])